Hi Xhevdet,
I am pretty sure it uses the http path during Ilias setup. You can view this in your ilias.ini.php located in /path/to/ilias/ilias.ini.php.
Look under the [server] configuration section, it should have this:
[server]
http_path = "http://localhost"
Change that to your domain name. If you are using cache'ing, its a good idea to clear that out if you don't see the change reflected in the emails. To clear the server cache for APC, you can either restart apache or visit apc.php and clear the cache from the GUI.
Regards,
Adam